From cb98727554695ca428a59a0c38593bc403c354e6 Mon Sep 17 00:00:00 2001 From: antux18 Date: Fri, 19 Jul 2024 15:23:00 +0200 Subject: [PATCH] Added artifacts_json to git ignore and deleting, closing #15. Deleted old YAML files. Added hints on the config template. --- .gitignore | 1 + artifacts_json/breitweiser_high.json | 38 ------------------- artifacts_json/isakov_taxonomy.json | 13 ------- artifacts_json/moses_high.json | 24 ------------ artifacts_json/parasyris_approximate.json | 19 ---------- artifacts_json/template.json | 23 ----------- artifacts_json/test.json | 24 ------------ artifacts_json/wang_tgopt.json | 19 ---------- artifacts_json/ziogas_deinsum-cpu.json | 37 ------------------ artifacts_json/ziogas_deinsum-gpu.json | 32 ---------------- artifacts_nickel/template.ncl | 6 +-- ...on_via_high_level_parallel_constructs.yaml | 7 ---- ...agent_based_simulation_with_BioDynaMo.yaml | 8 ---- ..._for_temporal_graph_attention_network.yaml | 8 ---- ...ces_in_hpc_io_machine_learning_models.yaml | 8 ---- ...he_lens_of_uncertainty_quantification.yaml | 8 ---- ...y_io_optimal_multi_linear_algebra-cpu.yaml | 7 ---- ...y_io_optimal_multi_linear_algebra-gpu.yaml | 7 ---- artifacts_yaml/template.yaml | 14 ------- artifacts_yaml/test.yaml | 15 -------- 20 files changed, 4 insertions(+), 314 deletions(-) delete mode 100644 artifacts_json/breitweiser_high.json delete mode 100644 artifacts_json/isakov_taxonomy.json delete mode 100644 artifacts_json/moses_high.json delete mode 100644 artifacts_json/parasyris_approximate.json delete mode 100644 artifacts_json/template.json delete mode 100644 artifacts_json/test.json delete mode 100644 artifacts_json/wang_tgopt.json delete mode 100644 artifacts_json/ziogas_deinsum-cpu.json delete mode 100644 artifacts_json/ziogas_deinsum-gpu.json delete mode 100644 artifacts_yaml/ppopp23/gpu_to_cpu_transpilation_and_optimization_via_high_level_parallel_constructs.yaml delete mode 100644 artifacts_yaml/ppopp23/high_performance_and_scalable_agent_based_simulation_with_BioDynaMo.yaml delete mode 100644 artifacts_yaml/ppopp23/tgopt_redundancy_aware-optimizations_for_temporal_graph_attention_network.yaml delete mode 100644 artifacts_yaml/sc22/a_taxonomy_of_error_sources_in_hpc_io_machine_learning_models.yaml delete mode 100644 artifacts_yaml/sc22/approximate_copmuting_through_the_lens_of_uncertainty_quantification.yaml delete mode 100644 artifacts_yaml/sc22/deinsum_practially_io_optimal_multi_linear_algebra-cpu.yaml delete mode 100644 artifacts_yaml/sc22/deinsum_practially_io_optimal_multi_linear_algebra-gpu.yaml delete mode 100644 artifacts_yaml/template.yaml delete mode 100644 artifacts_yaml/test.yaml diff --git a/.gitignore b/.gitignore index 8f89ce5..67d7189 100644 --- a/.gitignore +++ b/.gitignore @@ -3,6 +3,7 @@ output/* cache/* examples/* .snakemake/* +artifacts_json/* pkglist.csv log.txt build_status.csv \ No newline at end of file diff --git a/artifacts_json/breitweiser_high.json b/artifacts_json/breitweiser_high.json deleted file mode 100644 index 20758f6..0000000 --- a/artifacts_json/breitweiser_high.json +++ /dev/null @@ -1,38 +0,0 @@ -{ - "artifact_url": "https://zenodo.org/record/7544675/files/SF2-code.tar.gz", - "dockerfile_location": "bdm-paper-examples/docker", - "doi": "10.1145/3572848.3577480", - "git_packages": [ - { - "location": "~/.pyenv", - "name": "pyenv" - } - ], - "image_name": "bdm-publication-image-v7", - "misc_packages": [ - { - "name": "NetLogo-6.2.0-64", - "type": "tar", - "url": "http://ccl.northwestern.edu/netlogo/6.2.0/NetLogo-6.2.0-64.tgz" - }, - { - "name": "root_v6.22.06_python3.9_ubuntu-20.04", - "type": "tar", - "url": "http://biodynamo-lfs.web.cern.ch/biodynamo-lfs/third-party/root_v6.22.06_python3.9_ubuntu-20.04.tar.gz" - }, - { - "name": "qt_v5.12.10_ubuntu-20.04", - "type": "tar", - "url": "http://biodynamo-lfs.web.cern.ch/biodynamo-lfs/third-party/qt_v5.12.10_ubuntu-20.04.tar.gz" - }, - { - "name": "paraview_v5.9.0_ubuntu-20.04_default", - "type": "tar", - "url": "http://biodynamo-lfs.web.cern.ch/biodynamo-lfs/third-party/paraview_v5.9.0_ubuntu-20.04_default.tar.gz" - } - ], - "package_managers": [ - "dpkg" - ], - "type": "tar" -} diff --git a/artifacts_json/isakov_taxonomy.json b/artifacts_json/isakov_taxonomy.json deleted file mode 100644 index fd948ec..0000000 --- a/artifacts_json/isakov_taxonomy.json +++ /dev/null @@ -1,13 +0,0 @@ -{ - "artifact_url": "https://zenodo.org/record/6632461/files/SC22_artifacts_submission.zip", - "dockerfile_location": "SC22_artifacts_submission", - "doi": "10.5555/3571885.3571906", - "git_packages": [], - "image_name": "taxo:artefact", - "misc_packages": [], - "package_managers": [ - "dpkg", - "pip" - ], - "type": "zip" -} diff --git a/artifacts_json/moses_high.json b/artifacts_json/moses_high.json deleted file mode 100644 index 1a8505a..0000000 --- a/artifacts_json/moses_high.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "artifact_url": "https://zenodo.org/record/7508499/files/wsmoses/PolygeistGPU-Docker-v0.2.1.zip", - "dockerfile_location": "wsmoses-PolygeistGPU-Docker-ba18197/MocCUDA", - "doi": "10.1145/3572848.3577475", - "git_packages": [ - { - "location": "/root/MocCUDA", - "name": "MocCUDA" - } - ], - "image_name": "polygeist:artefact", - "misc_packages": [ - { - "name": "cmake-3.23.1", - "type": "tar", - "url": "https://github.com/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1.tar.gz" - } - ], - "package_managers": [ - "dpkg", - "pip" - ], - "type": "zip" -} diff --git a/artifacts_json/parasyris_approximate.json b/artifacts_json/parasyris_approximate.json deleted file mode 100644 index fc4d9d8..0000000 --- a/artifacts_json/parasyris_approximate.json +++ /dev/null @@ -1,19 +0,0 @@ -{ - "artifact_url": "https://zenodo.org/record/6926481/files/koparasy/HPAC-v0.0.0-Puppeteer.zip", - "dockerfile_location": "koparasy-HPAC-2723bb8/approx/puppeteer/container", - "doi": "10.5555/3571885.3571974", - "git_packages": [], - "image_name": "puppeteer:artefact", - "misc_packages": [ - { - "name": "HPAC", - "type": "zip", - "url": "https://github.com/koparasy/HPAC/archive/refs/heads/develop.zip" - } - ], - "package_managers": [ - "dpkg", - "pip" - ], - "type": "zip" -} diff --git a/artifacts_json/template.json b/artifacts_json/template.json deleted file mode 100644 index a8f33eb..0000000 --- a/artifacts_json/template.json +++ /dev/null @@ -1,23 +0,0 @@ -{ - "artifact_url": "https://example.com/artifact.zip", - "dockerfile_location": "path/to/docker/folder", - "doi": "...", - "git_packages": [ - { - "location": "path/to/git/repo", - "name": "pkg1" - } - ], - "image_name": "image:version", - "misc_packages": [ - { - "name": "mpkg1", - "type": "zip", - "url": "https://" - } - ], - "package_managers": [ - "dpkg" - ], - "type": "zip" -} diff --git a/artifacts_json/test.json b/artifacts_json/test.json deleted file mode 100644 index 1e6e029..0000000 --- a/artifacts_json/test.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "artifact_url": "http://localhost/artifact.zip", - "dockerfile_location": "./", - "doi": "...", - "git_packages": [ - { - "location": "/pkg1", - "name": "pkg1" - } - ], - "image_name": "prog:latest", - "misc_packages": [ - { - "name": "mpkg1", - "type": "zip", - "url": "http://localhost/package1.zip" - } - ], - "package_managers": [ - "dpkg", - "pip" - ], - "type": "zip" -} diff --git a/artifacts_json/wang_tgopt.json b/artifacts_json/wang_tgopt.json deleted file mode 100644 index 7d5723e..0000000 --- a/artifacts_json/wang_tgopt.json +++ /dev/null @@ -1,19 +0,0 @@ -{ - "artifact_url": "https://zenodo.org/record/7328505/files/tgopt-artifact.tgz", - "dockerfile_location": "tgopt-artifact", - "doi": "10.1145/3572848.3577490", - "git_packages": [], - "image_name": "tgopt:artefact", - "misc_packages": [ - { - "name": "Miniconda3-py37_4.12.0-Linux-x86_64", - "type": "zip", - "url": "https://repo.anaconda.com/miniconda/Miniconda3-py37_4.12.0-Linux-x86_64.sh" - } - ], - "package_managers": [ - "dpkg", - "conda" - ], - "type": "tar" -} diff --git a/artifacts_json/ziogas_deinsum-cpu.json b/artifacts_json/ziogas_deinsum-cpu.json deleted file mode 100644 index fffd608..0000000 --- a/artifacts_json/ziogas_deinsum-cpu.json +++ /dev/null @@ -1,37 +0,0 @@ -{ - "artifact_url": "https://zenodo.org/record/7004393/files/deinsum/sc22-artifact-0.4.zip", - "dockerfile_location": "deinsum-sc22-artifact-7559901/docker_cpu", - "doi": "10.5555/3571885.3571918", - "git_packages": [ - { - "location": "/dace", - "name": "dace" - }, - { - "location": "/multilinear-algebra-sc22-artifact", - "name": "multilinear-algebra-sc22-artifact" - }, - { - "location": "/ctf", - "name": "ctf" - } - ], - "image_name": "deinsum:artefact-cpu", - "misc_packages": [ - { - "name": "mpich-3.1.4", - "type": "tar", - "url": "http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz" - }, - { - "name": "Python-3.10.2", - "type": "tar", - "url": "https://www.python.org/ftp/python/3.10.2/Python-3.10.2.tgz" - } - ], - "package_managers": [ - "dpkg", - "pip" - ], - "type": "zip" -} diff --git a/artifacts_json/ziogas_deinsum-gpu.json b/artifacts_json/ziogas_deinsum-gpu.json deleted file mode 100644 index a4b9be7..0000000 --- a/artifacts_json/ziogas_deinsum-gpu.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "artifact_url": "https://zenodo.org/record/7004393/files/deinsum/sc22-artifact-0.4.zip", - "dockerfile_location": "deinsum-sc22-artifact-7559901/docker_gpu", - "doi": "10.5555/3571885.3571918", - "git_packages": [ - { - "location": "/dace", - "name": "dace" - }, - { - "location": "/multilinear-algebra-sc22-artifact", - "name": "multilinear-algebra-sc22-artifact" - }, - { - "location": "/ctf", - "name": "ctf" - } - ], - "image_name": "deinsum:artefact_gpu", - "misc_packages": [ - { - "name": "pip", - "type": "zip", - "url": "https://bootstrap.pypa.io/get-pip.py" - } - ], - "package_managers": [ - "dpkg", - "pip" - ], - "type": "zip" -} diff --git a/artifacts_nickel/template.ncl b/artifacts_nickel/template.ncl index 921c003..cac8851 100644 --- a/artifacts_nickel/template.ncl +++ b/artifacts_nickel/template.ncl @@ -1,15 +1,15 @@ let { Artifact, .. } = import "../workflow/nickel/artifact_contract.ncl" in { artifact_url = "https://example.com/artifact.zip", - type = "zip", + type = "zip", # Possible values: zip, tar doi = "...", image_name = "image:version", dockerfile_location = "path/to/docker/folder", - package_managers = [ "dpkg" ], + package_managers = [ "dpkg" ], # Possible values: dpkg, rpm, pacman, pip, conda git_packages = [ { name = "pkg1", location = "path/to/git/repo"} ], misc_packages = [ - { name = "mpkg1", url = "http://example.com/package.zip", type = "zip" } + { name = "mpkg1", url = "http://example.com/package.zip", type = "zip" # Possible values: zip, tar } ] } | Artifact diff --git a/artifacts_yaml/ppopp23/gpu_to_cpu_transpilation_and_optimization_via_high_level_parallel_constructs.yaml b/artifacts_yaml/ppopp23/gpu_to_cpu_transpilation_and_optimization_via_high_level_parallel_constructs.yaml deleted file mode 100644 index 5d2c69d..0000000 --- a/artifacts_yaml/ppopp23/gpu_to_cpu_transpilation_and_optimization_via_high_level_parallel_constructs.yaml +++ /dev/null @@ -1,7 +0,0 @@ -artifact_url: "https://zenodo.org/record/7508499/files/wsmoses/PolygeistGPU-Docker-v0.2.1.zip" -type: "zip" -doi: "10.1145/3572848.3577475" -image_name: "polygeist:artefact" -dockerfile_location: "wsmoses-PolygeistGPU-Docker-ba18197/MocCUDA" -package_managers: - - "dpkg" diff --git a/artifacts_yaml/ppopp23/high_performance_and_scalable_agent_based_simulation_with_BioDynaMo.yaml b/artifacts_yaml/ppopp23/high_performance_and_scalable_agent_based_simulation_with_BioDynaMo.yaml deleted file mode 100644 index 306ffb2..0000000 --- a/artifacts_yaml/ppopp23/high_performance_and_scalable_agent_based_simulation_with_BioDynaMo.yaml +++ /dev/null @@ -1,8 +0,0 @@ -artifact_url: "https://zenodo.org/record/7544675/files/SF2-code.tar.gz" -type: "tar" -doi: "10.1145/3572848.3577480" -image_name: "bdm-publication-image-v7" -dockerfile_location: "bdm-paper-examples/docker" -package_managers: - - "dpkg" -# Build done by running build.sh and not just docker build, but this is not implemented yet \ No newline at end of file diff --git a/artifacts_yaml/ppopp23/tgopt_redundancy_aware-optimizations_for_temporal_graph_attention_network.yaml b/artifacts_yaml/ppopp23/tgopt_redundancy_aware-optimizations_for_temporal_graph_attention_network.yaml deleted file mode 100644 index b3177b2..0000000 --- a/artifacts_yaml/ppopp23/tgopt_redundancy_aware-optimizations_for_temporal_graph_attention_network.yaml +++ /dev/null @@ -1,8 +0,0 @@ -artifact_url: "https://zenodo.org/record/7328505/files/tgopt-artifact.tgz" -type: "tar" -doi: "10.1145/3572848.3577490" -image_name: "tgopt:artefact" -dockerfile_location: "tgopt-artifact" -package_managers: - - "dpkg" - - "conda" diff --git a/artifacts_yaml/sc22/a_taxonomy_of_error_sources_in_hpc_io_machine_learning_models.yaml b/artifacts_yaml/sc22/a_taxonomy_of_error_sources_in_hpc_io_machine_learning_models.yaml deleted file mode 100644 index 01ff1a4..0000000 --- a/artifacts_yaml/sc22/a_taxonomy_of_error_sources_in_hpc_io_machine_learning_models.yaml +++ /dev/null @@ -1,8 +0,0 @@ -artifact_url: "https://zenodo.org/record/6632461/files/SC22_artifacts_submission.zip" -type: "zip" -doi: "10.5555/3571885.3571906" -image_name: "taxo:artefact" -dockerfile_location: "SC22_artifacts_submission" -package_managers: - - "dpkg" - - "pip" diff --git a/artifacts_yaml/sc22/approximate_copmuting_through_the_lens_of_uncertainty_quantification.yaml b/artifacts_yaml/sc22/approximate_copmuting_through_the_lens_of_uncertainty_quantification.yaml deleted file mode 100644 index 6817201..0000000 --- a/artifacts_yaml/sc22/approximate_copmuting_through_the_lens_of_uncertainty_quantification.yaml +++ /dev/null @@ -1,8 +0,0 @@ -artifact_url: "https://zenodo.org/record/6926481/files/koparasy/HPAC-v0.0.0-Puppeteer.zip" -type: "zip" -doi: "10.5555/3571885.3571974" -image_name: "puppeteer:artefact" -dockerfile_location: "koparasy-HPAC-2723bb8/approx/puppeteer/container" -package_managers: - - "dpkg" - - "pip" diff --git a/artifacts_yaml/sc22/deinsum_practially_io_optimal_multi_linear_algebra-cpu.yaml b/artifacts_yaml/sc22/deinsum_practially_io_optimal_multi_linear_algebra-cpu.yaml deleted file mode 100644 index e447282..0000000 --- a/artifacts_yaml/sc22/deinsum_practially_io_optimal_multi_linear_algebra-cpu.yaml +++ /dev/null @@ -1,7 +0,0 @@ -artifact_url: "https://zenodo.org/record/7004393/files/deinsum/sc22-artifact-0.4.zip" -type: "zip" -doi: "10.5555/3571885.3571918" -image_name: "deinsum:artefact-cpu" -dockerfile_location: "deinsum-sc22-artifact-7559901/docker_cpu" -package_managers: - - "dpkg" diff --git a/artifacts_yaml/sc22/deinsum_practially_io_optimal_multi_linear_algebra-gpu.yaml b/artifacts_yaml/sc22/deinsum_practially_io_optimal_multi_linear_algebra-gpu.yaml deleted file mode 100644 index 38e4039..0000000 --- a/artifacts_yaml/sc22/deinsum_practially_io_optimal_multi_linear_algebra-gpu.yaml +++ /dev/null @@ -1,7 +0,0 @@ -artifact_url: "https://zenodo.org/record/7004393/files/deinsum/sc22-artifact-0.4.zip" -type: "zip" -doi: "10.5555/3571885.3571918" -image_name: "deinsum:artefact_gpu" -dockerfile_location: "deinsum-sc22-artifact-7559901/docker_gpu" -package_managers: - - "dpkg" \ No newline at end of file diff --git a/artifacts_yaml/template.yaml b/artifacts_yaml/template.yaml deleted file mode 100644 index d0fe17f..0000000 --- a/artifacts_yaml/template.yaml +++ /dev/null @@ -1,14 +0,0 @@ -artifact_url: "https://example.com/artifact.zip" -type: "zip" # Possible values: zip, tar -doi: "XX.XXXX/XXXXXXX.XXXXXXX" -image_name: "image1:version" -dockerfile_location: "path/to/docker/folder" -package_managers: - - "dpkg" # Possible values: dpkg, rpm, pacman, pip, conda -git_packages: - - name: "pkg1" - location: "path/to/git/repo" -misc_packages: - - name: "mpkg1" - url: "https://example.com/package1.zip" - type: "zip" # Possible values: zip, tar diff --git a/artifacts_yaml/test.yaml b/artifacts_yaml/test.yaml deleted file mode 100644 index 1b6df18..0000000 --- a/artifacts_yaml/test.yaml +++ /dev/null @@ -1,15 +0,0 @@ -artifact_url: "http://localhost/artifact.zip" -type: "zip" -doi: "XX.XXXX/XXXXXXX.XXXXXXX" -image_name: "prog:latest" -dockerfile_location: "./" -package_managers: - - "dpkg" - - "pip" -git_packages: - - name: "pkg1" - location: "/pkg1" -misc_packages: - - name: "mpkg1" - url: "http://localhost/package1.zip" - type: "zip" \ No newline at end of file